Variant report

Variant	rs34000399
Chromosome Location	chr14:104101417-104101418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104096516..104099228-chr14:104099460..104101440,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10459574	0.89[ASN][1000 genomes]
rs11540512	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11844466	0.91[AFR][1000 genomes]
rs11846404	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11846838	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11851000	0.89[AFR][1000 genomes]
rs11851616	0.91[AFR][1000 genomes]
rs12147645	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12590968	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12884809	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12888993	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12889731	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12892038	0.91[AFR][1000 genomes]
rs12896171	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1606	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1799796	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273175	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2295152	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3212024	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212038	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212076	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3212090	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34843146	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35011804	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35921969	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4525427	0.91[AFR][1000 genomes]
rs4900590	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4900591	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4900592	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4906347	0.81[AFR][1000 genomes]
rs4906350	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906356	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57072546	0.87[AFR][1000 genomes]
rs60249782	0.87[AFR][1000 genomes]
rs61637848	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7148857	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs729438	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8021229	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34000399	KLC1	Cis_1M	lymphoblastoid	RTeQTL
rs34000399	RP11-73M18.8	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104096600-104118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:104097400-104101800	Weak transcription	Primary B cells from cord blood	blood
3	chr14:104097400-104102200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr14:104097400-104103600	Weak transcription	Liver	Liver
5	chr14:104097400-104104000	Weak transcription	HepG2	liver
6	chr14:104097400-104104200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:104097400-104104200	Weak transcription	Aorta	Aorta
8	chr14:104097400-104104200	Weak transcription	Brain Anterior Caudate	brain
9	chr14:104097400-104104200	Weak transcription	Stomach Mucosa	stomach
10	chr14:104097400-104104200	Weak transcription	Thymus	Thymus
11	chr14:104097400-104104200	Weak transcription	NH-A	brain
12	chr14:104097400-104105000	Weak transcription	Fetal Lung	lung
13	chr14:104097400-104107400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:104097400-104107800	Strong transcription	Fetal Stomach	stomach
15	chr14:104097400-104117800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr14:104097400-104119400	Weak transcription	HSMMtube	muscle
17	chr14:104097400-104120000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:104097400-104120000	Weak transcription	HUVEC	blood vessel
19	chr14:104097400-104120200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr14:104097400-104120200	Weak transcription	Colonic Mucosa	Colon
21	chr14:104097400-104120200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr14:104097400-104120400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr14:104097400-104120400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr14:104097400-104120800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr14:104097600-104101600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr14:104097600-104102200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:104097600-104106200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:104098000-104102600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr14:104098200-104103000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr14:104098600-104102600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr14:104098600-104119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:104098600-104119800	Weak transcription	K562	blood
34	chr14:104098800-104104200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr14:104098800-104104400	Weak transcription	HMEC	breast
36	chr14:104099000-104101600	Enhancers	Brain Hippocampus Middle	brain
37	chr14:104099000-104102400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr14:104099200-104102200	Enhancers	Adipose Nuclei	Adipose
39	chr14:104099200-104102400	Enhancers	Left Ventricle	heart
40	chr14:104099200-104102600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr14:104099200-104102800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr14:104099200-104104800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr14:104099200-104120200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr14:104099400-104102000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:104099400-104104000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr14:104099400-104104000	Weak transcription	Pancreas	Pancrea
47	chr14:104099400-104104200	Weak transcription	A549	lung
48	chr14:104099600-104101600	Genic enhancers	NHLF	lung
49	chr14:104099600-104102400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr14:104099600-104102600	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links